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CHECK report for ProCoNA on veracruz1

This page was generated on 2018-04-12 13:37:29 -0400 (Thu, 12 Apr 2018).

Package 1068/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.16.0
David L Gibbs
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ProCoNA
Branch: RELEASE_3_6
Last Commit: 08a38fd
Last Changed Date: 2017-10-30 12:40:08 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ProCoNA
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ProCoNA_1.16.0.tar.gz
StartedAt: 2018-04-12 07:52:57 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:57:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 260.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ProCoNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ProCoNA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ProCoNA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProCoNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProCoNA’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ProCoNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bootstrapProconaNetwork: no visible global function definition for
  ‘as.dist’
bootstrapProconaNetwork: no visible global function definition for
  ‘cutreeDynamic’
buildProconaNetwork: no visible global function definition for
  ‘as.dist’
buildProconaNetwork: no visible global function definition for
  ‘cutreeDynamic’
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for ‘pdf’
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for ‘dev.off’
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for ‘par’
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for ‘pdf’
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for ‘dev.off’
getFisherMatrix,character-character-numeric-numeric: no visible global
  function definition for ‘fisher.test’
peptideConnectivityTest,proconaNet-data.frame-character-character-numeric:
  no visible global function definition for ‘t.test’
peptideCorrelationTest,matrix-data.frame-character-character: no
  visible global function definition for ‘t.test’
Undefined global functions or variables:
  as.dist cutreeDynamic dev.off fisher.test par pdf t.test
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "as.dist", "fisher.test", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
correlationWithPhenotypesHeatMap 5.986  0.131   6.188
bootstrapProconaNetwork          5.831  0.062   5.967
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ProCoNA.Rcheck/00check.log’
for details.



Installation output

ProCoNA.Rcheck/00install.out

* installing *source* package ‘ProCoNA’ ...
** R
** data
** inst
** preparing package for lazy loading
==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* DONE (ProCoNA)

Tests output

ProCoNA.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ProCoNA") || stop("unable to load MyPackage")
Loading required package: ProCoNA
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.4.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

Loading required package: flashClust

Attaching package: 'flashClust'

The following object is masked from 'package:fastcluster':

    hclust

The following object is masked from 'package:stats':

    hclust


Attaching package: 'ProCoNA'

The following object is masked from 'package:ProtGenerics':

    peptides

The following object is masked from 'package:Biobase':

    samples

[1] TRUE
> BiocGenerics:::testPackage("ProCoNA")
Constructing New ProCoNA Network Object
Using power: 1

Computing adjacency
Computing TOM
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Clustering
 ..cutHeight not given, setting it to 0.461  ===>  99% of the (truncated) height range in dendro.
 ..done.

  0   1   2   3   4 
  4 174 127  92  77 
Merging modules
 mergeCloseModules: Merging modules whose distance is less than 0.1
   .. will look for grey label ME0
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
    Changing original colors:
        1 to  1
        2 to  2
        3 to  3
        4 to  4
   Calculating new MEs...
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 0
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
Topological Overlap Permutation Test On Modules
Permuting module: 1

   dim of TOM: 174174

Permuting module: 2

   dim of TOM: 127127

Permuting module: 3

   dim of TOM: 9292

Permuting module: 4

   dim of TOM: 7777

DONE!
[1] "module analysis:  1"
[1] "probes that pass Kme and are within module: 122"
[1] "of these, 26 are relevant to our PI network..."
[1] "found  4  in the first column"
[1] "found  3  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.034"
[1] "*****"
[1] "module analysis:  2"
[1] "probes that pass Kme and are within module: 123"
[1] "of these, 65 are relevant to our PI network..."
[1] "found  6  in the first column"
[1] "found  8  in the second column"
[1] "6  observed edges"
[1] "pvalue:  0"
[1] "*****"
[1] "module analysis:  3"
[1] "probes that pass Kme and are within module: 92"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  0"
[1] "probes that pass Kme and are within module: 4"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  4"
[1] "probes that pass Kme and are within module: 74"
[1] "of these, 8 are relevant to our PI network..."
[1] "found  2  in the first column"
[1] "found  1  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.01"
[1] "*****"
Permuting module: 1

   dim of TOM: 100100

Permuting module: 2

   dim of TOM: 100100

Permuting module: 3

   dim of TOM: 100100

Permuting module: 4

   dim of TOM: 100100

Permuting module: 5

   dim of TOM: 100100



RUNIT TEST PROTOCOL -- Thu Apr 12 07:57:13 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ProCoNA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.969   0.588  17.168 

Example timings

ProCoNA.Rcheck/ProCoNA-Ex.timings

nameusersystemelapsed
MMvsPS0.3530.0150.379
MMvsPSallModules0.0010.0000.001
accessors0.1810.0080.191
bootstrapProconaNetwork5.8310.0625.967
buildProconaNetwork3.0940.0913.225
compareNetworksWithFishersExactTest0.0010.0000.001
compareNetworksWithFishersExactTestProcona0.0000.0000.001
corBootstrap1.0720.0151.102
correlationWithPhenotypesHeatMap5.9860.1316.188
getFisherMatrix0.3080.0140.324
goStatTest0.0010.0010.001
hclust0.0010.0000.002
moduleMemberCorrelations0.2060.0110.220
modulePhenotypeCorrelations0.2090.0100.232
peptideConnectivityTest1.8090.1571.993
peptideCorrelationTest2.4910.0832.616
plotNet0.1880.0100.198
ppiPermTest0.2500.0100.261
printNet000
subsetPeptideData0.2930.1040.406
toPermTest0.4040.0460.459
utri0.0010.0000.001